Mass Effect 2 : The Council of Varda
by N7 Dragon
Summary: What if Cerberus was infiltrated while Shepard was being rebuilt? What if they rescued the Commander before Cerberus could activate her? Well they did, and the Galaxy is never going to be the same again.  Rated M for safety.


**AN: This is a very AU fanfic that both loosely and closely follows the events of Mass Effect 2. It should be obvious that I do not in any way own any part it. **

**There will be references to the works of Tolkien, which are used heavily as inspiration for the Council of Varda (you'll learn about them in later chapters), as well as any of the Star Trek series - excluding the originals and the most recent movie. Bonus points to anyone who finds these references and points them out in reviews. You do not need to be familiar with these works to understand what is going on but they will add depth, I hope. Laugh at my ships designation: CVS, please.**

**Chapter 1**

**The Second Coming **

It is said that there are times when things are bad, then really bad. After that things can to be said 'hellish' and 'oh shit.' Right now was one of those 'Holly fucking shit, hell just froze over and Lucifer thinks my backyard is the best place to set up shop.'

Predictably very few people in the galaxy knew of the impending doom, and of those only a few of those actually believed it. (sigh) ... The Reapers were coming and the galaxy had their collective heads up their asses. The great and wise Citadel Council who had saved the galaxy from the Rachni and the Krogan Rebellions and served to keep a close watch on the Terminus Systems for all of their citizens, Council Species or otherwise, had decided to ignore the cycle of death for galactic civilizations. Understandable of course. Very little evidence existed beyond what landed in their lap as pieces of Sovereign. It seemed that their brush with the Grim Reaper didn't affect the Citadel Council's decision on a real one.

(sigh) I look out the window at the school below, cursing and blessing the decision to place the offices of the High Council next to a children's school. The little ones laughed and played and chased and ran in circles, never really knowing about the sad eyes that would stare out at them as hard choices were made. The teachers knew of course, as did the parents. They were the ones that had built both the High Council chambers as well as the school. They knew the choices that had to be made. These choices needed to be supervised by at least a conscious.

One of those choices needed to be made. Undercover operatives had infiltrated the only other independent organization trying to do something. Cerberus. They had obtained the body of the famous hero Commander Elayne Shepard, the Council Spectre. Reports revealed that the Illusive Man had decided to rebuild the Commander under the operation name of 'the Lazarus Project', and then aim her at the Reapers. I suppose he hoped that the Spectre would chase all the bad nightmares back under the bed for him. Almost as bad as the Citadel Council. No, that was too harsh...Shepard is important, as a symbol to rally behind. A symbol to trust, of hope. Still, too pin all of his efforts into one individual is out of character for him. Its the reason hell's forecast dropped into the negatives.

The project is staffed by some of the best of Humanity had to offer and funded enough to lower the poverty rate on Earth by twenty percent. It was headed by Miranda Lawson of course, the Illusive Man couldn't afford to trust it to any one else, and she kept a tight watch on her cell. Our own operatives had barely passed her inspection.

But, we were not the only ones to have infiltrated to Lazarus Cell. Doctor Wilson, the Chief Medical Officer of Lawson's cell and main reason that Shepard was now breathing, had attempted to hack the stations security mecs. What his goal was and who his master is hard to gather as his attempt was thwarted by one of our operatives. Its rather difficult to interrogate a man with half of his brain blown away. Lawson was quite upset to say the least but our man had done nothing wrong, and even received a commendation from the Illusive Man himself! That had many of us laughing, even today the recording still cracks a smirk in the People's faces.

Our man was now in a better, more trusted position in the Lazarus cell. And with Shepard's increasingly frequent bouts of consciousness we needed to make a move.

I look outside my window again. The human children, the elven childs, the fairies that loved to swoop down and catch tufts of hair leaving cries of joy in their wake. Life on Varda is amazing.

But this life may all change with this one choice. One touch to the console and the plan would be set in motion and life would never be the same again. For anyone.

But so is it true with all great choices.

The computer chimes in confirmation as the order is sent. I cross the room and fill myself a glass of venerable wine. "So it begins..."

_Lazarus Station_

_Operative Gwain's Quarters_

A pop up appears on the extranet screen. A face turns and sees with trained eyes the following message from the junk mail's porn subscription.

_Execute Order Edain_

The link is closed. A hard face requests Operatives Jones and Kowalski to meet him in his office for a diagnostic report. Several minutes later they arrive and the meeting go's just like any other meeting between the Chief of Engineering and his subordinates. The meeting degenerates, as they were prone to do so among the engineering staff, into a discussion on the merits of Old Human literature, with Gwain dropping several key words. The orders are relayed and no suspicion is held by the listening Miranda Lawson.

At 0005 hours that night the security mecs are hacked again while everyone off duty sleeps deeply with the aid of certain sedatives added to dinner The medical team is out cold before they know they are betrayed, engineering powers down critical systems and security was fed loops of sensory data from six months ago. All the while three starships decloak two clicks from the station.

Boarding parties quickly take control of the station and Shepard is secured and transferred to the Vingilot's waiting sick bay. The station database is downloaded with minimal hacking with Operative Gwain's clearance, just below Lawson's. All of the Cerberus personnel are taken prisoner. Lawson is not happy of course and has to be restrained with biotic restrictors. No casualties on either side.

And then Shepard began to regain consciousness again.

"Captain," a voice resounded on the Bridge. "You are needed in sick bay."

Captain Eärendil turned from leaning over the helm with Ensign Mayweather and left the CIC to his XO.

Entering sick bay proved to be rather hazardous as the Commander proved she had just as much control over her biotics now as she did two years ago.

"What the hell is going on!" Screamed Shepard as she held several technicians inches from the ceiling. Eärendil quickly signaled Bach, the ship's AI, to not engage any sort of violent response.

Doctor Aran calmly spoke "Commander please remain calm, you have been in a coma for the last two year. If you continue you may induce an arrest." The medical monitor seemed to agree as Shepard's heartbeat pushed into the red zone.

For a moment it seemed that Shepard would acquiesce. Her biotic aura receded back within her skin and the rather scared technicians floated to the floor. Until she then saw that Operative Gwain, who had come to check on his mission objective, was still in his former uniform.

The room glowed a pale violet that pulsated with the raging monitors. The poor medical techs resumed their previous position on the ceiling after being knocked out by the impact.

Shepard said only one word. "Cerberus."

Captain Eärendil quickly replied from the doorway, "No Commander he is not Cerberus. The Lieutenant was part of a unit that had infiltrated Cerberus." Eärendil looked at Gwain significantly, who had the decency to blush slightly. The Captain then turned to regard the Commander who had yet to free the biotic power warping the air. "You are aboard my ship the CVS Vingilot. Please calm down and all will be explained."

The Spectre slowly released her hold on the swirling dark energy. The monitors soon quieted as she centered herself. "Start talking." The techs continued to float near the ceiling. The effort of containing the power had taken its toll as she leaned against her bio bed.

Eärendil stepped inside, the doors closed behind him. "Your former command, the Normandy was destroyed while on patrol for Geth over the planet of Alchera. Do you remember that Commander?"

The Spectre's became clouded in memory. She had launched the distress beacon and had been fighting fires with Liara. She sent her to the escape pods and then saved Joker. But, she didn't make it into the pod with him. The attacking ship had then fired and separated her from the open hatch. The pod had been jettisoned with Joker inside while her air escaped from the tears in her hardsuit. Gasping ... choking ...

The Commander snapped out of the memory as a hand came to rest on her shoulder. Gwain had become disturbed by the sight of the woman becoming so consumed by the memory.

"I remember." Shepard didn't shake the hand off. The eyes full of pity were also ignored by the Spectre.

"You died Shepard, your body was recovered and then rebuilt. Please listen to the full story before you bring out the biotics again."

Shepard slowly nodded and Gwain removed his hand. The techs fell slowly into the bio beds around the room. The Captain gave Shepard a grateful look before continuing.

"Cerberus rebuilt you Commander. We were aware of this and had decided to observe and be prepared for any foul play. Our plan was to rescue you after they had completed their work."

Shepard looked past the Captain and absently said "Two years."

"Yes Commander, two years have passed since your death."

The Spectre regained the sharpness in her eye. "What did Cerberus do to put me back together?"

Gwain coughed and Shepard turned to him. "I think that I can explain that part Commander." After receiving a nod from both Shepard and Eärendil he continued. "You were rebuilt by an initiative by the Illusive Man known as the Lazarus project. It consisted of the best in cutting-edge technology as well as the best medical minds of the century. Most of your organs and tissues are natural but there is a significant number of cybernetic implants that were used to speed your ... recovery. Cerberus has poured billions of credits into you Shepard. And we just stole all that right from under their noses." The Intelligence operative smiled at the last statement.

Shepard couldn't help but smirk as well. Any blow to the rogue black ops was worthy of a smile. But her forehead creased into a frown. "Who are you people, what kind of designation is CVS?"

The sick bay was silent for a moment as all eyes turned to the Captain, the most piercing were those of the Commander. A deep breath later and he began to explain.

"The designation CVS stands for Council of Varda's Ship. Varda is our homeworld and the focal point of our government. This can all be explained in greater detail later, but please Commander, lets just leave the subject for the time being for a more private atmosphere."

Shepard was very obviously not happy with this response but nodded her head anyway. "I'll hold you to that sir." Despite her apparent fatigue Shepard's eyes glowed in that promise.

Eärendil smiled thinly at the response and ordered what remained of the conscious personnel out of the room with Shepard's victims. They seemed only too happy to vacate the kill zone.

The Spectre sighed once they had cleared out. "Cerberus prisoners can be quite the handful Commander, please understand," were the Captain's last words before the door closed behind them.

For a long time nothing was said between Gwain and Shepard. Until the Commander caught a rather disturbing thought.

"Did Cerberus leave anything inside of me that I need to worry about? It would really suck if I suddenly turned all Terra Firma." Memories of a blue asari flitted through her mind with joy, longing and trepidation. Thoughts of a reunion were quickly scattered though, for now.

Gwain looked slightly perturbed as he sat down on the Doctor's desk, moving aside several stacks of pads and OSDs. With every word his voice withdrew from the air. "I'm not sure Shepard, logically the Illusive Man would have ensured his control through some method. Whether this came from an implant or more subtle means, I don't know." The last syllables were barely more than a whisper. Clearly the thought was unhinging the Lieutenant's confidence.

The response didn't seem to make the Commander to feel any better of course. "What do you mean more subtle?" The air seemed to twist about again with the slice of her question. Her eyes were starting to glow a luminous amethyst. Gwain only looked at the Spectre with a great amount of regret.

The sight registered with Shepard. The air resumed its previous patterns but her eyes continued to pulse with dark energy.

"You were saying Lieutenant ..."

"Gwain, Lieutenant Calon Gwain... What I meant by more subtle means was some sort of mental imprint or conditioning. Or something as simple as manipulation of available information. Tests will be needed before we know any form of certainty."

Shepard was very clearly not happy, but her eyes returned to their light moss color. She knew what he

"How can I trust you to give me _accurate_ tests? Or for anything at all for that matter?"

At this Gwain smirked. This he could understand. This he could deal with.

"Commander there is no sure way of gaining your trust in what time we have to spare before we return to Vardinian space. But, you have full clearance to all of our systems and databases until we speak with the Council."

"The Citadel Council?"

The Lieutenant grinned.

"No Commander, the Council of Varda. Its a long story, one that you can find the answer to from Bach, or if you prefer I'm sure that the Captain would be more than happy to inform you our government along with answering any other questions you may have."

"Ok...wait Bach?..."

But the Lieutenant had already passed through the door, leaving the swoosh of the metal plates behind him and a confused Spectre with her artificial tour guide. Leaving Shepard alone, even while confused, would allow her to come to a few conclusions as well as prepare her next set of questions. None would attempt to influence these decisions of course. With someone like the Commander they were as likely to back fire as they were to succeed.

Shepard gazed at the closed door with heavy eyes. Exhaustion from two years of death and reconstruction had taken their toll. The tired woman's body eased itself into a bio bed and immediately descended into blissful dreams of a blue asari. As soon as the REM cycles were confirmed Bach activated the scanners and began a full examination. The Commander would resist the process otherwise; besides as long as there were no immediate concerns the AI would insure that the entire procedure remained confidential. After all there was no need to upset the ever deadly Spectre.


End file.
